DESCRIPTION

Package: pictographPlus
Type: Package
Title: Tumor evolution drives intra-tumor heterogeneity, yet functional clone-specific profiles remain poorly understood. We developed PICTographPlus, a computational tool that integrates bulk DNA and RNA sequencing to reconstruct clone-specific transcriptomic profiles and uncover functional transitions between clones, offering a powerful framework for cancer evolution studies. 
Version: 1.0.0
Author: Jiaying Lai
Maintainer: The package maintainer <jlai33@jh.edu>
Description: This package is used to perform tumor evolution reconstruction using genomic data. In addition, the tool can also estimate clone-level RNA expression from bulk-RNA data.
License: MIT
Encoding: UTF-8
LazyData: true
Imports:
  readr (>= 2.1.4),
  tidyverse (>= 2.0.0),
  dplyr (>= 1.1.1),
  tidyr (>= 1.3.0),
  LaplacesDemon (>= 16.1.6),
  igraph (>= 2.0.1),
  viridis (>= 0.6.5),
  ggmcmc (>= 1.5.1),
  UpSetR (>= 1.4.0),
  cluster (>= 2.1.4),
  fgsea (>= 1.32.0),
  ggrepel (>= 0.9.6),
  diptest (>= 0.77-1),
  pheatmap (>= 1.0.12),
  DESeq2 (>= 1.46.0),
  purrr (>= 1.0.2),
  GenomicRanges (>= 1.58.0),
  IRanges (>= 2.40.1)
RoxygenNote: 7.3.2